recompute_some_chains.py
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#!python3
import subprocess, os, sys
# Put a list of problematic chains here, they will be properly deleted and recomputed
problems = [
"7nhm_1_A_1-2923"
"4wfa_1_X_1-2923"
"4wce_1_X_1-2923"
]
# provide the path to your data folders, the RNANet.db file, and the RNANet.py file as arguments to this script
path_to_3D_data = sys.argv[1]
path_to_seq_data = sys.argv[2]
path_to_db = sys.argv[3]
path_to_RNANet = sys.argv[4]
for p in problems:
print()
print()
print()
print()
homology = ('-' in p) # H4cky l1f3
# Remove the datapoints files and 3D files
subprocess.run(["rm", '-f', path_to_3D_data + f"/rna_mapped_to_Rfam/{p}.cif"])
subprocess.run(["rm", '-f', path_to_3D_data + f"/rna_only/{p}.cif"])
files = [ f for f in os.listdir(path_to_3D_data + "/datapoints") if p in f ]
for f in files:
subprocess.run(["rm", '-f', path_to_3D_data + f"/datapoints/{f}"])
# Find more information
structure = p.split('_')[0]
chain = p.split('_')[2]
if homology:
families = [ f.split('.')[1] for f in files ] # The RFAM families this chain has been mapped onto
# Delete the chain from the database, and the associated nucleotides and re_mappings, using foreign keys
for fam in families:
command = ["sqlite3", path_to_db, f"PRAGMA foreign_keys=ON; delete from chain where structure_id=\"{structure}\" and chain_name=\"{chain}\" and rfam_acc=\"{fam}\";"]
print(' '.join(command))
subprocess.run(command)
command = ["python3.8", path_to_RNANet, "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "--redundant", "-r", "20.0", "--extract", "--only", p]
else:
# Delete the chain from the database, and the associated nucleotides and re_mappings, using foreign keys
command = ["sqlite3", path_to_db, f"PRAGMA foreign_keys=ON; delete from chain where structure_id=\"{structure}\" and chain_name=\"{chain}\" and rfam_acc is null;"]
print(' '.join(command))
subprocess.run(command)
command = ["python3.8", path_to_RNANet, "--3d-folder", path_to_3D_data, "--seq-folder", path_to_seq_data, "--redundant", "-r", "20.0", "--no-homology", "--extract", "--only", p]
# Re-run RNANet
os.chdir(os.path.dirname(os.path.realpath(path_to_db)) + '/../')
print('\n',' '.join(command),'\n')
subprocess.run(command)